From d25622940c2da39e3a2959cfdba6571dc5f4a535 Mon Sep 17 00:00:00 2001
From: Pietro Incardona <incardon@mpi-cbg.de>
Date: Tue, 3 Nov 2015 18:35:38 +0100
Subject: [PATCH] Cleaning code
---
configure.ac | 6 +
m4/immdx_lib_parmetis.m4 | 85 +++++++++++++
openfpm_data | 2 +-
src/Decomposition/BasicDecomposition.hpp | 146 ++++++++++++++---------
src/Makefile.am | 6 +-
5 files changed, 182 insertions(+), 63 deletions(-)
create mode 100644 m4/immdx_lib_parmetis.m4
diff --git a/configure.ac b/configure.ac
index 878255775..4da0b7c59 100644
--- a/configure.ac
+++ b/configure.ac
@@ -30,6 +30,7 @@ m4_ifdef([ACX_MPI],,[m4_include([m4/acx_mpi.m4])])
m4_ifdef([AX_OPENMP],,[m4_include([m4/ax_openmp.m4])])
m4_ifdef([AX_CUDA],,[m4_include([m4/ax_cuda.m4])])
m4_ifdef([IMMDX_LIB_METIS],,[m4_include([m4/immdx_lib_metis.m4])])
+m4_ifdef([IMMDX_LIB_PARMETIS],,[m4_include([m4/immdx_lib_parmetis.m4])])
CXXFLAGS+=" --std=c++11 "
NVCCFLAGS=" "
@@ -105,6 +106,11 @@ fi
IMMDX_LIB_METIS([],[echo "Cannot detect metis, use the --with-metis option if it is not installed in the default location"
exit 201])
+## Check for parMetis
+
+IMMDX_LIB_PARMETIS([],[echo "Cannot detect parmetis, use the --with-parmetis option if it is not installed in the default location"
+ exit 203])
+
####### include OpenFPM_devices include path
INCLUDES_PATH+="-I. -Isrc/config/ -I../openfpm_io/src -I../openfpm_data/src -I../openfpm_devices/src -I../openfpm_vcluster/src/"
diff --git a/m4/immdx_lib_parmetis.m4 b/m4/immdx_lib_parmetis.m4
new file mode 100644
index 000000000..aaf101257
--- /dev/null
+++ b/m4/immdx_lib_parmetis.m4
@@ -0,0 +1,85 @@
+AC_DEFUN([IMMDX_LIB_PARMETIS], [
+ AC_MSG_CHECKING(for PARMETIS library)
+ AC_REQUIRE([AC_PROG_CC])
+ #
+ # User hints...
+ #
+ AC_ARG_VAR([PARMETIS], [PARMETIS library location])
+ AC_ARG_WITH([parmetis],
+ [AC_HELP_STRING([--with-parmetis],
+ [user defined path to PARMETIS library])],
+ [
+ if test -n "$PARMETIS" ; then
+ AC_MSG_RESULT(yes)
+ with_parmetis=$PARMETIS
+ elif test "$withval" != no ; then
+ AC_MSG_RESULT(yes)
+ with_parmetis=$withval
+ else
+ AC_MSG_RESULT(no)
+ fi
+ ],
+ [
+ if test -n "$PARMETIS" ; then
+ with_parmetis=$PARMETIS
+ AC_MSG_RESULT(yes)
+ else
+ with_parmetis=/usr
+ if test ! -f "$with_parmetis/include/parmetis.h" ; then
+ with_parmetis=/usr/local
+ if test ! -f "$with_parmetis/include/parmetis.h" ; then
+ with_parmetis=""
+ AC_MSG_RESULT(failed)
+ else
+ AC_MSG_RESULT(yes)
+ fi
+ else
+ AC_MSG_RESULT(yes)
+ fi
+ fi
+ ])
+ #
+ # locate PARMETIS library
+ #
+ if test -n "$with_parmetis" ; then
+ old_CC=$CC
+ old_CFLAGS=$CFLAGS
+ old_LDFLAGS=$LDFLAGS
+ CFLAGS="-I$with_parmetis/include -I$with_metis/include"
+ LDFLAGS="-L$with_parmetis/lib -L$with_metis/lib"
+ CC=$CXX
+
+ AC_LANG_SAVE
+ AC_LANG_C
+
+ AC_CHECK_LIB(parmetis, ParMETIS_V3_PartKway,
+ [parmetis_lib=yes], [parmetis_lib=yes], [-lm])
+ AC_CHECK_HEADER(parmetis.h, [parmetis_h=yes],
+ [parmetis_h=no], [/* check */])
+
+ AC_LANG_RESTORE
+
+ CFLAGS=$old_CFLAGS
+ LDFLAGS=$old_LDFLAGS
+ CC=$old_CC
+
+ AC_MSG_CHECKING(PARMETIS in $with_parmetis)
+ if test "$parmetis_lib" = "yes" -a "$parmetis_h" = "yes" ; then
+ AC_SUBST(PARMETIS_INCLUDE, [-I$with_parmetis/include])
+ AC_SUBST(PARMETIS_LIB, [-L$with_parmetis/lib])
+ AC_MSG_RESULT(ok)
+ else
+ AC_MSG_RESULT(failed)
+ fi
+ fi
+ #
+ #
+ #
+ if test x = x"$PARMETIS_LIB" ; then
+ ifelse([$2],,[AC_MSG_ERROR(Failed to find valid PARMETIS library)],[$2])
+ :
+ else
+ ifelse([$1],,[AC_DEFINE(HAVE_PARMETIS,1,[Define if you have PARMETIS library])],[$1])
+ :
+ fi
+ ])dnl IMMDX_LIB_PARMETIS
diff --git a/openfpm_data b/openfpm_data
index ec562d96b..778bdb9c9 160000
--- a/openfpm_data
+++ b/openfpm_data
@@ -1 +1 @@
-Subproject commit ec562d96b376389ebc4024112671c05e265d23d0
+Subproject commit 778bdb9c9b59b81b193152c7284687a98afb7503
diff --git a/src/Decomposition/BasicDecomposition.hpp b/src/Decomposition/BasicDecomposition.hpp
index 594b85df3..4bbecdf25 100644
--- a/src/Decomposition/BasicDecomposition.hpp
+++ b/src/Decomposition/BasicDecomposition.hpp
@@ -129,6 +129,15 @@ private:
//! Cell-list that store the geometrical information of the local internal ghost boxes
CellList<dim, T, FAST> lgeo_cell;
+ static void * message_receive(size_t msg_i ,size_t total_msg, size_t total_p, size_t i, size_t ri, void * ptr)
+ {
+ openfpm::vector<openfpm::vector<idx_t>> * v = static_cast<openfpm::vector<openfpm::vector<idx_t>> *>(ptr);
+
+ v->get(i).resize(msg_i/sizeof(idx_t));
+
+ return &(v->get(i).get(0));
+ }
+
/*! \brief Constructor, it decompose and distribute the sub-domains across the processors
*
* \param v_cl Virtual cluster, used internally for communications
@@ -153,8 +162,7 @@ private:
}
//! MPI initialization
- int MPI_PROC_ID = 0;
- MPI_Comm_rank(MPI_COMM_WORLD, &MPI_PROC_ID);
+ size_t MPI_PROC_ID = v_cl.getProcessUnitID();
// Here we use PARMETIS
// Create a cartesian grid graph
@@ -215,49 +223,45 @@ private:
MPI_Request *requests_send = new MPI_Request[Np];
MPI_Status *statuses = new MPI_Status[Np];
- //-----------------------------------------------
-
- /*
-
- /* create a type for struct nm_v */
- const int nitems = 9;
- int blocklengths[9] = {1,1};
- MPI_Datatype types[9] = {MPI_INT, MPI_INT, MPI_INT, MPI_INT, MPI_INT, MPI_INT, MPI_INT, MPI_INT, MPI_INT};
- MPI_Datatype MPI_VERTEX_TYPE;
- MPI_Aint offsets[9];
-
- offsets[0] = offsetof(nm_v, x);
- offsets[1] = offsetof(nm_v, y);
- offsets[2] = offsetof(nm_v, z);
- offsets[3] = offsetof(nm_v, communication);
- offsets[4] = offsetof(nm_v, computation);
- offsets[5] = offsetof(nm_v, memory);
- offsets[6] = offsetof(nm_v, id);
- offsets[7] = offsetof(nm_v, sub_id);
- offsets[8] = offsetof(nm_v, proc_id);
-
- MPI_Type_create_struct(nitems, blocklengths, offsets, types, &MPI_VERTEX_TYPE);
- MPI_Type_commit(&MPI_VERTEX_TYPE);
-
- //-----------------------------------------------
-
// Prepare vector of arrays to contain all partitions
- int **partitions = new int*[Np];
+
+ openfpm::vector<openfpm::vector<idx_t>> partitions(Np);
+ partitions.get(MPI_PROC_ID).resize(sub_g.getNVertex());
+ std::copy(partition,partition+sub_g.getNVertex(),&partitions.get(MPI_PROC_ID).get(0));
+
+ openfpm::vector<size_t> prc;
+ openfpm::vector<size_t> sz;
+ openfpm::vector<void *> ptr;
+
+ for (size_t i = 0 ; i < Np ; i++)
+ {
+ if (i != v_cl.getProcessUnitID())
+ {
+ prc.add(i);
+ sz.add(sub_g.getNVertex() * sizeof(idx_t));
+ ptr.add(partitions.get(MPI_PROC_ID).getPointer());
+ }
+ }
+
+
+ v_cl.sendrecvMultipleMessagesNBX(prc.size(),&sz.get(0),&prc.get(0),&ptr.get(0),message_receive,&partitions,NONE);
+
+/* idx_t **partitions = new idx_t*[Np];
partitions[MPI_PROC_ID] = partition;
for (int i = 0; i < Np; i++) {
if (i != MPI_PROC_ID)
- partitions[i] = new int[gp.getNVertex()];
- }
-
+ partitions[i] = new idx_t[gp.getNVertex()];
+ }*/
+
// Exchange partitions with other processors
- exchangePartitions(partitions, gp.getNVertex(), sub_g.getNVertex(), requests_recv, requests_send, statuses, MPI_PROC_ID, Np);
+// exchangePartitions(partitions, gp.getNVertex(), sub_g.getNVertex(), requests_recv, requests_send, statuses, MPI_PROC_ID, Np);
// Init data structure to keep trace of new vertices distribution in processors (needed to update main graph)
- std::vector<size_t> *v_per_proc = new std::vector<size_t>[Np];
-
+ openfpm::vector<openfpm::vector<size_t>> v_per_proc(Np);
+
// Update graphs with the new distributions
updateGraphs(partitions, gp, sub_g, v_per_proc, vtxdist, statuses, MPI_PROC_ID, Np);
-
+
if (MPI_PROC_ID == 0) {
VTKWriter<Graph_CSR<nm_v, nm_e>, GRAPH> gv2(gp);
gv2.write("test_graph_2.vtk");
@@ -272,10 +276,12 @@ private:
gp.reset_map_ids();
// Renumbering main graph
- for (size_t p = 0; p < Np; p++) {
- for (size_t j = vtxdist[p], i = 0; j < vtxdist[p + 1]; j++, i++) {
- gp.set_map_ids(j, gp.vertex(v_per_proc[p][i]).template get<nm_v::id>());
- gp.vertex(v_per_proc[p][i]).template get<nm_v::id>() = j;
+ for (size_t p = 0; p < Np; p++)
+ {
+ for (size_t j = vtxdist[p], i = 0; j < vtxdist[p + 1]; j++, i++)
+ {
+ gp.set_map_ids(j, gp.vertex(v_per_proc.get(p).get(i)).template get<nm_v::id>());
+ gp.vertex(v_per_proc.get(p).get(i)).template get<nm_v::id>() = j;
}
}
@@ -293,30 +299,57 @@ private:
// Get result partition for this processor
partition = parmetis_graph.getPartition();
+ partitions.get(MPI_PROC_ID).resize(sub_g.getNVertex());
+ std::copy(partition,partition+sub_g.getNVertex(),&partitions.get(MPI_PROC_ID).get(0));
+
// Reset partitions array
- partitions[MPI_PROC_ID] = partition;
+/* partitions[MPI_PROC_ID] = partition;
for (int i = 0; i < Np; i++) {
if (i != MPI_PROC_ID) {
delete partitions[i];
partitions[i] = new int[gp.getNVertex()];
}
- }
+ }*/
// Reset data structure to keep trace of new vertices distribution in processors (needed to update main graph)
- for (int i = 0; i < Np; ++i) {
- v_per_proc[i].clear();
+ for (int i = 0; i < Np; ++i)
+ {
+ v_per_proc.get(i).clear();
}
// Exchange partitions with other processors
- exchangePartitions(partitions, gp.getNVertex(), sub_g.getNVertex(), requests_recv, requests_send, statuses, MPI_PROC_ID, Np);
+// exchangePartitions(partitions, gp.getNVertex(), sub_g.getNVertex(), requests_recv, requests_send, statuses, MPI_PROC_ID, Np);
+
+ prc.clear();
+ sz.clear();
+ ptr.clear();
+ for (size_t i = 0 ; i < Np ; i++)
+ {
+ if (i != v_cl.getProcessUnitID())
+ {
+ partitions.get(i).clear();
+ prc.add(i);
+ sz.add(sub_g.getNVertex() * sizeof(idx_t));
+
+// std::cout << "sub_g: " << sub_g.getNVertex() * sizeof(idx_t) << "\n";
+
+ ptr.add(partitions.get(MPI_PROC_ID).getPointer());
+ }
+ }
+
+ v_cl.sendrecvMultipleMessagesNBX(prc.size(),&sz.get(0),&prc.get(0),&ptr.get(0),message_receive,&partitions,NONE);
+
// Update graphs with the new distributions
updateGraphs(partitions, gp, sub_g, v_per_proc, vtxdist, statuses, MPI_PROC_ID, Np);
+
+ //
-
- if (MPI_PROC_ID == 0) {
+ if (MPI_PROC_ID == 1) {
VTKWriter<Graph_CSR<nm_v, nm_e>, GRAPH> gv2(gp);
gv2.write("test_graph_4.vtk");
+ bool test = compare("test_graph_4.vtk","test_graph_test.vtk");
+ BOOST_REQUIRE_EQUAL(test,true);
}
/*
@@ -634,9 +667,8 @@ private:
* \param proc_id current processors rank
* \param Np total umber of processors
*/
- void updateGraphs(int** &partitions,Graph_CSR<nm_v, nm_e> &gp, Graph_CSR<nm_v, nm_e> &sub_g, std::vector<size_t>* &v_per_proc, idx_t* &vtxdist, MPI_Status* &statuses, int proc_id, int Np) {
-
- int size_p = sub_g.getNVertex();
+ void updateGraphs(openfpm::vector<openfpm::vector<idx_t>> &partitions,Graph_CSR<nm_v, nm_e> &gp, Graph_CSR<nm_v, nm_e> &sub_g, openfpm::vector<openfpm::vector<size_t>> & v_per_proc, idx_t* &vtxdist, MPI_Status* &statuses, int proc_id, int Np)
+ {
int local_j = 0;
sub_g.clear();
@@ -648,26 +680,22 @@ private:
// Update main graph with other partitions made by Parmetis in other processors and the local partition
for (int i = 0; i < Np; i++) {
- int ndata = 0;
- MPI_Get_count(&statuses[i], MPI_INT, &ndata);
-
- if (i == proc_id)
- ndata = size_p;
+ int ndata = partitions.get(i).size();
// Update the main graph with received informations
for (int k = 0, l = vtxdist[i]; k < ndata && l < vtxdist[i + 1]; k++, l++) {
// Create new n_vtxdist (1) (just count processors vertices)
- n_vtxdist[partitions[i][k] + 1]++;
+ n_vtxdist[partitions.get(i).get(k) + 1]++;
// Update proc id in the vertex
- gp.vertexById(l).template get<nm_v::proc_id>() = partitions[i][k];
+ gp.vertexById(l).template get<nm_v::proc_id>() = partitions.get(i).get(k);
// Add vertex to temporary structure of distribution (needed to update main graph)
- v_per_proc[partitions[i][k]].push_back(gp.vertexById(l).template get<nm_v::id>());
+ v_per_proc.get(partitions.get(i).get(k)).add(gp.vertexById(l).template get<nm_v::id>());
// Add vertices belonging to this processor in sub graph
- if (partitions[i][k] == proc_id) {
+ if (partitions.get(i).get(k) == proc_id) {
nm_v pv = gp.vertexById(l);
sub_g.addVertex(pv);
diff --git a/src/Makefile.am b/src/Makefile.am
index 1cea7e7b9..c5ed683ec 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -1,10 +1,10 @@
-LINKLIBS = $(METIS_LIB) $(PTHREAD_LIBS) $(OPT_LIBS) $(BOOST_LDFLAGS) $(BOOST_IOSTREAMS_LIB) $(CUDA_LIBS)
+LINKLIBS = $(METIS_LIB) $(PTHREAD_LIBS) $(OPT_LIBS) $(BOOST_LDFLAGS) $(BOOST_IOSTREAMS_LIB) $(CUDA_LIBS) $(PARMETIS_LIB)
noinst_PROGRAMS = pdata
pdata_SOURCES = main.cpp ../openfpm_devices/src/memory/HeapMemory.cpp ../openfpm_devices/src/memory/PtrMemory.cpp ../openfpm_vcluster/src/VCluster.cpp ../openfpm_data/src/Memleak_check.cpp
-pdata_CXXFLAGS = $(CUDA_CFLAGS) $(INCLUDES_PATH) $(METIS_INCLUDE) -I/home/antonio/Documents/openfpm/dependencies/PARMETIS/include $(BOOST_CPPFLAGS) -Wno-unused-function
+pdata_CXXFLAGS = $(CUDA_CFLAGS) $(INCLUDES_PATH) $(METIS_INCLUDE) $(PARMETIS_INCLUDE) $(BOOST_CPPFLAGS) -Wno-unused-function
pdata_CFLAGS = $(CUDA_CFLAGS)
-pdata_LDADD = $(LINKLIBS) -L/usr/lib/x86_64-linux-gnu/ -lmetis -lboost_iostreams -lboost_program_options -L/home/antonio/Documents/openfpm/dependencies/PARMETIS/lib -lparmetis
+pdata_LDADD = $(LINKLIBS) -L/usr/lib/x86_64-linux-gnu/ -lmetis -lboost_iostreams -lboost_program_options -lparmetis
nobase_include_HEADERS = Decomposition/BasicDecomposition.hpp Decomposition/CartDecomposition.hpp Decomposition/common.hpp Decomposition/Decomposition.hpp Decomposition/ie_ghost.hpp \
Decomposition/nn_processor.hpp Decomposition/ie_loc_ghost.hpp Decomposition/ORB.hpp \
Graph/CartesianGraphFactory.hpp \
--
GitLab